I am confused.

You said you knew full well of the check in time restrictions at JFK, and yet you arrived at the airport during its busiest time only 30 minutes prior to baggage cutoff? Should they have charged you? Absolutely. Why? There were a myriad of ways to avoid this situation. First, I am assuming that you were trying to check in in the main atrium area of T3. There are a few other locations that you can check in at besides that main entrance, even including your home. You are able to check in online, even if you have an infant. If you don't have a printer that works, or you didn't make it to Office Depot that morning, did you try using the kiosks? Even in the busiest of times, once you have your boarding pass, I've witnessed how quick the bag drop lines moves (yes, I used kennedy and quick in the same sentence).

And while I absolutely think they should have charged you, I think the $50 SDC fee pp would have been more appropriate (since, after all, it is the next flight).

zz